Description

LIM homeobox 9 [Source:HGNC Symbol;Acc:HGNC:14222]

INSDC coordinates

chromosome:GRCh38:CM000663.2:197911902:197935478:1

About this gene

This gene has 8 transcripts (splice variants), 64 orthologues, 11 paralogues, is a member of 4 Ensembl protein families and is associated with 104 phenotypes.

NameTranscript IDbpProteinTranslation IDBiotypeCCDSUniProtRefSeqFlags
LHX9-004ENST000003673877836397aaENSP00000356357
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS1393Q9NQ69 NM_020204
NP_064589
TSL:1

Transcript Support Level 1, when transcripts are supported by at least one non-suspect mRNA.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).APPRIS P3

PRINCIPAL3 - APPRIS candidate principal isoform (earliest CCDS).

APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods.

LHX9-001ENST000003673907413388aaENSP00000356360
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS30962Q9NQ69 NM_001014434
NP_001014434
TSL:1

Transcript Support Level 1, when transcripts are supported by at least one non-suspect mRNA.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).APPRIS ALT1

ALTERNATIVE1 - APPRIS candidate principal isoform that is conserved in at least three tested non-primate species.

APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods.

LHX9-007ENST000005611732144336aaENSP00000453064
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-H0YL54 -TSL:5

Transcript Support Level 5, for transcripts that are not supported at all by either an mRNA or an EST.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).
LHX9-003ENST000003673911623321aaENSP00000356361
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-Q9NQ69 -TSL:5

Transcript Support Level 5, for transcripts that are not supported at all by either an mRNA or an EST.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).
LHX9-005ENST0000036738875854aaENSP00000356358
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-H0Y330 -TSL:2

Transcript Support Level 2, when transcripts are supported by multiple ESTs or by an mRNA flagged as suspect.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).
LHX9-009ENST0000060612743137aaENSP00000483170
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-A0A087X083 -CDS 3' incomplete3' truncation in transcript evidence prevents annotation of the end of the CDS.TSL:3

Transcript Support Level 3, when transcripts are supported by a single EST only.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

LHX9-006ENST0000047572725926aaENSP00000482898
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
---CDS 3' incomplete3' truncation in transcript evidence prevents annotation of the end of the CDS.TSL:1

Transcript Support Level 1, when transcripts are supported by at least one non-suspect mRNA.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

LHX9-010ENST000006155201051No protein-
 
Retained intronAlternatively spliced transcript that is believed to contain intronic sequence relative to other coding transcripts in a given locus.
---TSL:NA

Transcript Support Level Not Analysed. Pseudogenes, single exon transcripts, HLA, T-cell receptor and Ig transcripts are not analysed and therefore not given any of the TSL categories.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

Gene-based displays